def predict_proba(self, X):
"""Predict probabilities for classes from X.
:param array2d X: prediction input features
"""
check_is_fitted(self)
X = check_array(X)
self._check_n_features(X, reset=False)
result = ranger.ranger(
self.tree_type_,
np.asfortranarray(X.astype("float64")),
np.asfortranarray([[]]),
self.feature_names_, # variable_names
self.mtry_,
self.n_estimators, # num_trees
self.verbose,
self.seed,
self.n_jobs_, # num_threads
False, # write_forest
self.importance_mode_,
self.min_node_size,
self.split_select_weights or [],
bool(self.split_select_weights), # use_split_select_weights
[], # always_split_variable_names
False, # use_always_split_variable_names
True, # prediction_mode
self.ranger_forest_["forest"], # loaded_forest
np.asfortranarray([[]]), # snp_data
self.replace, # sample_with_replacement
False, # probability
self.categorical_features_, # unordered_feature_names
bool(self.categorical_features_), # use_unordered_features
self.save_memory,
self.split_rule_,
[], # case_weights
False, # use_case_weights
self.class_weights or [],
False, # predict_all
self.keep_inbag,
[1], # sample_fraction
0.5, # alpha
0.1, # minprop
self.holdout,
1, # prediction_type
self.num_random_splits,
False, # use_sparse_data
self.order_snps_,
self.oob_error,
self.max_depth,
self.inbag or [],
bool(self.inbag), # use_inbag
self.regularization_factor_,
self.use_regularization_factor_,
self.regularization_usedepth,
)
predictions = np.atleast_2d(np.array(result["predictions"]))
return predictions[:, self.ranger_class_order_]
def _get_terminal_node_forest(self, X):
"""Get a terminal node forest for X.
:param array2d X: prediction input features
"""
# many fields defaulted here which are unused
forest = ranger.ranger(
self.tree_type_,
np.asfortranarray(X.astype("float64")),
np.asfortranarray([[]]),
self.feature_names_, # variable_names
0, # m_try
self.n_estimators, # num_trees
self.verbose,
self.seed,
self.n_jobs_, # num_threads
False, # write_forest
0, # importance_mode
0, # min_node_size
[], # split_select_weights
False, # use_split_select_weights
[], # always_split_feature_names
False, # use_always_split_feature_names
True, # prediction_mode
self.ranger_forest_["forest"], # loaded_forest
np.asfortranarray([[]]), # snp_data
True, # sample_with_replacement
False, # probability
[], # unordered_feature_names
False, # use_unordered_features
False, # save_memory
1, # split_rule
[], # case_weights
False, # use_case_weights
[], # class_weights
False, # predict_all
self.keep_inbag,
[1], # sample_fraction
0, # alpha
0, # minprop
self.holdout,
2, # prediction_type (terminal nodes)
1, # num_random_splits
False, # use_sparse_data
False, # order_snps_
False, # oob_error
0, # max_depth
[], # inbag
False, # use_inbag
[], # regularization_factor_
False, # use_regularization_factor_
False, # regularization_usedepth
)
return forest
def fit(self, X, y, sample_weight=None):
"""Fit the ranger random forest using training data.
:param array2d X: training input features
:param array1d y: training input targets
:param array1d sample_weight: optional weights for input samples
"""
self.tree_type_ = 3 # tree_type, TREE_REGRESSION
# Check input
X, y = self._validate_data(X, y)
# Check the init parameters
self._validate_parameters(X, y, sample_weight)
if sample_weight is not None:
sample_weight = _check_sample_weight(sample_weight, X)
use_sample_weight = True
# ranger does additional rng on samples if weights are passed.
# if the weights are ones, then we dont want that extra rng.
if np.array_equal(np.unique(sample_weight), np.array([1.0])):
sample_weight = []
use_sample_weight = False
else:
sample_weight = []
use_sample_weight = False
# Set X info
self.feature_names_ = [str(c).encode() for c in range(X.shape[1])]
self._check_n_features(X, reset=True)
if self.always_split_features is not None:
always_split_features = [
str(c).encode() for c in self.always_split_features
]
else:
always_split_features = []
# Fit the forest
self.ranger_forest_ = ranger.ranger(
self.tree_type_,
np.asfortranarray(X.astype("float64")),
np.asfortranarray(np.atleast_2d(y).astype("float64").transpose()),
self.feature_names_, # variable_names
self.mtry_,
self.n_estimators, # num_trees
self.verbose,
self.seed,
self.n_jobs_, # num_threads
True, # write_forest
self.importance_mode_,
self.min_node_size,
self.split_select_weights or [],
bool(self.split_select_weights), # use_split_select_weights
always_split_features, # always_split_feature_names
bool(always_split_features), # use_always_split_feature_names
False, # prediction_mode
{}, # loaded_forest
np.asfortranarray([[]]), # snp_data
self.replace, # sample_with_replacement
False, # probability
self.categorical_features_, # unordered_feature_names
bool(self.categorical_features_), # use_unordered_features
self.save_memory,
self.split_rule_,
sample_weight, # case_weights
use_sample_weight, # use_case_weights
[], # class_weights
False, # predict_all
self.keep_inbag,
self.sample_fraction_,
self.alpha,
self.minprop,
self.holdout,
1, # prediction_type
self.num_random_splits,
False, # use_sparse_data
self.order_snps_,
self.oob_error,
self.max_depth,
self.inbag or [],
bool(self.inbag), # use_inbag
self.regularization_factor_,
False, # use_regularization_factor
self.regularization_usedepth,
)
if self.quantiles:
forest = self._get_terminal_node_forest(X)
terminal_nodes = np.array(forest["predictions"]).astype(int)
self.random_node_values_ = np.empty(
(np.max(terminal_nodes) + 1, self.n_estimators))
self.random_node_values_[:] = np.nan
for tree in range(self.n_estimators):
idx = np.arange(X.shape[0])
np.random.shuffle(idx)
self.random_node_values_[terminal_nodes[idx, tree],
tree] = y[idx]
return self
def fit(self, X, y, sample_weight=None):
"""Fit the ranger random forest using training data.
:param array2d X: training input features
:param array2d y: training input targets, rows of (bool, float)
representing (survival, time)
:param array1d sample_weight: optional weights for input samples
"""
self.tree_type_ = 5 # tree_type, TREE_SURVIVAL
# Check input
X = check_array(X)
# convert 1d array of 2tuples to 2d array
# ranger expects the time first, and status second
# since we follow the scikit-survival convention, we fliplr
y = np.fliplr(np.array(y.tolist()))
# Check the init parameters
self._validate_parameters(X, y, sample_weight)
if sample_weight is not None:
sample_weight = _check_sample_weight(sample_weight, X)
use_sample_weight = True
# ranger does additional rng on samples if weights are passed.
# if the weights are ones, then we dont want that extra rng.
if np.array_equal(np.unique(sample_weight), np.array([1.0])):
sample_weight = []
use_sample_weight = False
else:
sample_weight = []
use_sample_weight = False
# Set X info
self.feature_names_ = [str(c).encode() for c in range(X.shape[1])]
self._check_n_features(X, reset=True)
if self.always_split_features is not None:
always_split_features = [
str(c).encode() for c in self.always_split_features
]
else:
always_split_features = []
# Fit the forest
self.ranger_forest_ = ranger.ranger(
self.tree_type_,
np.asfortranarray(X.astype("float64")),
np.asfortranarray(y.astype("float64")),
self.feature_names_, # variable_names
self.mtry_,
self.n_estimators, # num_trees
self.verbose,
self.seed,
self.n_jobs_, # num_threads
True, # write_forest
self.importance_mode_,
self.min_node_size,
self.split_select_weights or [],
bool(self.split_select_weights), # use_split_select_weights
always_split_features, # always_split_variable_names
bool(always_split_features), # use_always_split_variable_names
False, # prediction_mode
{}, # loaded_forest
np.asfortranarray([[]]), # snp_data
self.replace, # sample_with_replacement
False, # probability
self.categorical_features_, # unordered_feature_names
bool(self.categorical_features_), # use_unordered_features
False, # save_memory
self.split_rule_,
sample_weight, # case_weights
use_sample_weight, # use_case_weights
[], # class_weights
False, # predict_all
self.keep_inbag,
self.sample_fraction_,
self.alpha,
self.minprop,
self.holdout,
1, # prediction_type
self.num_random_splits,
False, # use_sparse_data
self.order_snps_,
self.oob_error,
self.max_depth,
self.inbag or [],
bool(self.inbag), # use_inbag
self.regularization_factor_,
False, # use_regularization_factor
self.regularization_usedepth,
)
self.event_times_ = np.array(
self.ranger_forest_["forest"]["unique_death_times"])
# dtype to suppress warning about ragged nested sequences
self.cumulative_hazard_function_ = np.array(
self.ranger_forest_["forest"]["cumulative_hazard_function"],
dtype=object)
return self
def fit(self, X, y, sample_weight=None):
"""Fit the ranger random forest using training data.
:param array2d X: training input features
:param array1d y: training input target classes
:param array1d sample_weight: optional weights for input samples
"""
self.tree_type_ = 9 # tree_type, TREE_PROBABILITY enables predict_proba
# Check input
X, y = self._validate_data(X, y)
check_classification_targets(y)
# Check the init parameters
self._validate_parameters(X, y, sample_weight)
if sample_weight is not None:
sample_weight = _check_sample_weight(sample_weight, X)
use_sample_weight = True
# ranger does additional rng on samples if weights are passed.
# if the weights are ones, then we dont want that extra rng.
if np.array_equal(np.unique(sample_weight), np.array([1.0])):
sample_weight = []
use_sample_weight = False
else:
sample_weight = []
use_sample_weight = False
# Map classes to indices
y = np.copy(y)
self.classes_, y = np.unique(y, return_inverse=True)
self.n_classes_ = len(self.classes_)
# Set X info
self.feature_names_ = [str(c).encode() for c in range(X.shape[1])]
self._check_n_features(X, reset=True)
if self.always_split_features is not None:
always_split_features = [
str(c).encode() for c in self.always_split_features
]
else:
always_split_features = []
# Fit the forest
self.ranger_forest_ = ranger.ranger(
self.tree_type_,
np.asfortranarray(X.astype("float64")),
np.asfortranarray(np.atleast_2d(y).astype("float64").transpose()),
self.feature_names_, # variable_names
self.mtry_,
self.n_estimators, # num_trees
self.verbose,
self.seed,
self.n_jobs_, # num_threads
True, # write_forest
self.importance_mode_,
self.min_node_size,
self.split_select_weights or [],
bool(self.split_select_weights), # use_split_select_weights
always_split_features, # always_split_variable_names
bool(always_split_features), # use_always_split_variable_names
False, # prediction_mode
{}, # loaded_forest
np.asfortranarray([[]]), # snp_data
self.replace, # sample_with_replacement
False, # probability
self.categorical_features_, # unordered_variable_names
bool(self.categorical_features_), # use_unordered_variable_names
self.save_memory,
self.split_rule_,
sample_weight, # case_weights
use_sample_weight, # use_case_weights
self.class_weights or [],
False, # predict_all
self.keep_inbag,
self.sample_fraction_,
0.5, # alpha, ignored because maxstat can't be used on classification
0.1, # minprop, ignored because maxstat can't be used on classification
self.holdout,
1, # prediction_type
self.num_random_splits,
False, # use_sparse_data
self.order_snps_,
self.oob_error,
self.max_depth,
self.inbag or [],
bool(self.inbag), # use_inbag
self.regularization_factor_,
False, # use_regularization_factor
self.regularization_usedepth,
)
self.ranger_class_order_ = np.argsort(
np.array(
self.ranger_forest_["forest"]["class_values"]).astype(int))
return self